This chapter reviews the complications of the most common systemic mycoses and subcutaneous mycoses, including histoplasmosis, coccidioidomycosis, paracoccidioidomycosis, blastomycosis, mycetoma, sporotrichosis, and chromoblastomycosis. Subcutaneous mycoses are chronic diseases of tropical and subtropical areas in which the etiologic agent is acquired after traumatic infection. Immunocompromised patients are very susceptible to the complications and sequelae of histoplasmosis. Osteomyelitis of the spine and tenosynovitis, mainly of the hands, may be present. Some of the chronic sequelae caused by the disease can be evidenced by radiological changes, such as osteopenia, joint space narrowing, bony destruction, and in some instances, ankylosis. Adequate treatment usually improves the patient condition, but in almost every case, the sequelae of the infection contribute to the morbidity of the disease. If the sequelae lesions harbor viable Paracoccidioides brasiliensis, relapses may occur. The complication rate of chromoblastomycosis is low, and probably in many cases, the disease is misdiagnosed, mostly as verrucous tuberculosis or the sequelae left by the surgical removal of the affected area. Secondary infection occurs in as many as 63% of patients with chromoblastomycosis. The complications and long-term sequelae of the extracutaneous form of sporotrichosis are rare and affect principally bones and weight-bearing joints, with or without tenosynovitis, periostitis, and ostheolisis. Fungemia is a rare complication generally associated with the disseminated form of the disease, although a few reports support the presence of the fungus in the bloodstream without evidence of disseminated sporotrichosis.